Midnight Prayers
by Angel16125
Summary: "He couldn’t help but look at the bed and think of all the nights they had shared together.Walking to the door he took one last look around at a place he was becoming very comfortable and happy in. A place he would never be in again, in the same capacity."
1. Chapter 1

A/N: This is my first X-Files FF. I've had this idea in my head for a while now, I'm a huge MulderScully shipper but sometimes I can see ScullyxSkinner happening. I do have ideas for more if this is received well soooo Please Review

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She doesn't know exactly when it happened. When his visits became more than just checking in on her and idle chit chat. When they crossed 'that line'.

Dana Scully looked over to where Walter Skinner was laying in bed beside her, fast asleep. She shook her head.

_What the hell am I doing?_

She was sleeping with her boss to distract herself from the loss she felt from Mulder's absence.

Mulder had been missing for seven months now. Scully refused to consider the possibility that he might be dead, even though everyone said it was highly likely at this point.

She knew this whole situation with Skinner was wrong. The worst part was, she was realizing that Skinner was starting to have feelings for her. He had started trying to display them by doing more 'boyfriendly' things. She tried to lie to herself that she had feelings for him in return, when she knew there was only enough room for one man in her heart and that man was not the one that so frequently shared her bed. Every time Skinner tried to show more affection for her outside of her bedroom she would push him away.

It was so easy at first, to pretend and let his kisses and caresses wash away some of the numbness she felt day after day. It always ended the same way though. She ended up sitting in bed feeling the numbness and grief returning with an increasing amount of guilt added in, while he slept peacefully beside her.

Scully slipped out of bed and quietly walked to the living room. Glancing at the clock she saw the time, 3:40 am. Another sleepless night.

If Mulder was here, she would be calling him right now saying she couldn't sleep, and he would gladly talk to her until she was so sleepy that she was falling asleep with her phone still in her hand.

But Mulder isn't here.

Scully was alone, even when there was a man in her bed.

She never talked to Skinner about her midnight insomnia. She knew he would willingly get up with her and do anything to help her, but that only made her feel worse, and the guilt she was feeling these days was almost becoming worse than the loss of her best friend.

Guilt over using her friend, and Boss for that matter, to try to feel something other than numbness pain.

Guilt over feeling like she was moving past Mulder by being with Skinner. Mulder, the one person she thought would always be with her, and someday hoped would be more than just her friend and partner.

She let her head fall back on the back of the couch and closed her eyes. She said her rehearsed nightly prayer that Mulder would come back to her somehow and that everything would go back to how it was.

A shadow fell over her face, but she didn't open her eyes. She couldn't handle looking into Skinner's caring eyes.

"Can't sleep?" He asked as he sat down next to her.

"Mmm."

"Want me to make you some tea?"

_What is wrong with me?_ She chastised herself.

Here is this nice caring man, that would do anything to make her feel better, it would seem, and she can't stop thinking about another man to give him an inch.

"No I'm fine." She lied. She was far from being fine, but no amount of tea is going to make her better.

The ringing of her cell phone broke through the silence in the room like a grenade.

Scully got up slowly to answer it, grateful for the distraction.

"Scully." She answered.

Skinner watched as a wave of emotion ran over Scully's face. He stood up and walked over to her. When he was about to reach out to her to offer support, she turned and walked away.

"Ok. I'll be right there." Scully said excitedly and hung up her phone.

She all but ran to her room to change without saying anything to Skinner.

"Dana? What is it?" He asked, even though he knew there was only thing that would make her so excited.

"Mulder." Scully said ripping off her camisole and pulling on a pair of jeans and t-shirt. "They found him." She grabbed her socks and ran to the living room to put them on along with her shoes. "He's as Pres. View in the ICU."

"Ok give me a second to change and I'll come with you." Skinner said turning to walk back to the bedroom.

"No." Scully said, quicker than she meant to, making him stop and turn back to her. "They said he is still out of it. I'll go check on him and give you a call."

She walked over to him and he could see the light start to return to her eyes. The light that had seemed to burn out the moment they lost Mulder over six months ago, and he knew she was slipping away from him.

"OK." He said forcing a smile. "I'll meet you up there later."

"Sounds good." Scully said with a smile. She leaned in and gave him a light kiss and was out the door before he could say anything else.

As the door closed, he knew deep down, he would never be in this apartment again like he is now. He knew, he would never hold Scully again. That quick kiss would be the last time her lips ever touched him.

She didn't say the words, but he knew.

They were over. If there ever was a 'them' to begin with.

Mulder always held her heart and he always would. While Skinner was able to share her bed and body for a time, he knew he never had a chance at sharing her heart.

While Skinner had been able to lie to himself that while Mulder was missing and presumed dead, he had a chance to win over the amazing Dana Scully, he knew there was never a chance when he watched her on the phone and when she told him Mulder was found.

The way she said 'Mulder'.

There was no mistaking the way it seemed like life was breathed back into her with the knowledge that he was alive and home.

Any chance he had of being with her any longer was yanked away in the last five minutes.

It was his own fault he felt like shit right now. He never should have allowed himself to fall for her. For that matter, he should have never started sleeping with her. He knew how much pain she was in. He could tell she was trying to find something, anything to hold on to. Something to reassure herself that she was still alive, and he was more than willing for that thing she clung onto, to be him.

Skinner walked back into her bedroom and got dressed. He couldn't help but look at the bed and think of all the nights they had shared together.

Walking to the door he took one last look around at a place he was becoming very comfortable and happy in. A place he would never be in again, in the same capacity.

"Good Bye, Dana." He said softly as he walked out the door. He knew he would never get the chance to tell her in person. She would never mention the time they shared. It didn't exist in a world that Mulder was alive.


	2. Chapter 2

A/N: I want to thank everyone that took the time to read Chapter 1! I appreciate the comments and encouragement to continue this story so here's Chapter 2!!!

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It had been two months since Mulder was found and Scully still couldn't believe it was true. She kept thinking at any moment she was going to wake up and this was just a dream. She had had so many dreams of them finding Mulder only to wake up to him still gone.

Scully looked up from her desk and glanced over to where Mulder sat behind his own desk.

_He's alive. He's safe. Everything that happened while he was missing was over… it never happened_… Scully told herself.

She knew she was being selfish and unfair to pretend everything that went in between Skinner and her never happened. She told herself that he must not mind, since he never tried to talk to her about anything other than work.

But she knew the truth.

He was taking her lead on how to approach the topic. Since she had left him that night in her apartment she never brought up the topic, so clearly it was over.

She knew she should feel guilty over pretty much, using him and then dropping him as soon as the as Mulder came back.

As Scully quickly snuck another glance at her partner and best friend she knew the only thing she was truly feeling guilty about was that, while she was sleeping with Skinner it felt like she was doing it behind Mulder's back. The guilt only increased while she avoided not telling Mulder what had happened.

It's not like there wasn't plenty of opportunities. She had stayed in the hospital with him for a week, only leaving to shower and change and even that took the nurses pushing her out the door.

After the week in the hospital, she practically moved into his apartment to take of him. He had recovered quickly but she still insisted on taking care of him, not wanting him to push himself too quickly. So many nights when they would talk and she never got the courage to tell him about Skinner. There even came a night when he asked what she had done while he was gone, jokingly asking if she found Mr. Right. Scully laughed it off but could feel the pain in her heart at thinking how he would feel if he knew the truth.

She had decided that night, he never could. Her and Skinner was over, and in her mind it never even happened. Maybe if she said it enough she could convince herself. She knew Skinner would never betray her and tell anyone.

_Let's face it he'd get into way more trouble for sleeping with a subordinate_. Scully thought bitterly.

So that was that, Mulder would never know the truth.

"Scully?"

Scully jerked her head up at the sound of her name.

"Yeah?"

"Jeez what where you thinking about? I've been trying to ask you about getting some lunch for five minutes." Mulder joked with a hint of concern.

"Uh. Nothing." Scully stumbled over her word. Trying to act busy with her paperwork.

"You okay?" He asked concern evident in his voice as he leaned closer to her.

"Yeah." She said forcing a smile. "My brain is just getting foggy from all this paperwork." She lied, "Lunch sounds great.

"You sure?"

"Yes." Scully laughed. "Aren't I the one that is supposed to be making sure your okay?"

Mulder smiled at her reaching for her hand. "We all need someone to make sure we are ok."

Scully looked down to where their hands touched then back up and Mulder. "Yeah I guess we do. But I'm fine."

"Okay." He said with a smile and a squeeze to her hand. "Then I say lunch."

"Do you want to order something?" Scully asked reaching into her desk for their usual take out place's take out menu.

"No. Let's get out of here." Mulder said standing up and grabbing his jacket off the back of his chair.

"Okay." She said joining him at the door.

He let her walk out first, like he always did and shut the door behind them.

Scully waited while he locked the door. After he was sure the door was locked Mulder took his usual place beside Scully. She couldn't help the small smile on her face when she felt him place his hand on the small of her back. His spot.

As they waited for the elevator she thought to herself.

It_ was just a fling. There's no need to tell him. It's over and will never happen again.__ There is no need to worry about it._.._ What's past should stay in the past... Right..?_


	3. Chapter 3

A/N: Thank you all for your comments. I hope you all enjoy chapter 3!! As always reviews and comments keep me motivated to write more!

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Mulder looked over at Scully, over his turkey melt and couldn't help but smile. He couldn't believe he was only gone for seven months. Every minute he was apart from her felt like an eternity. He was sure she was going to tell him it had been years when she told him how long he had been missing.

Thinking about Scully had been the one thing that had kept him going. Refusing to be a reason she would be sad was what got him through.

Looking at her he noticed something he hadn't noticed before. He had been so fixated on looking at her face that he hadn't notice the different jewelry she wore around her neck.

"Hey Scully did you get a new necklace?" He asked.

"Yeah, I lost mine a few months ago." Scully said irritated.

"I'm sorry." He said, knowing how meaningful the cross her mother gave her was.

"It's ok." She sighed, "It has to be somewhere in my place. I'm sure it will show up in time."

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Scully looked up at the clock on the wall. Finally it was 5 o'clock. She sighed and leaned back. She looked over at Mulder, who seemed to be deep in a file.

_Oh, please not a new case tonight, it's Friday night._

"Are you staying late?" Scully asked

"What?" Mulder asked, then saw the time. "Oh... Um... no, well... I want to finish looking this over."

"Need help?"

Mulder smiled at her offer. While he knew she didn't really want to, he knew she would stay if he asked.

"No I won't be long."

"Do you want me to bring over some pizza?" She asked hoping he said yes. She had stopped staying over at his place after he had come back to work, and she missed the time they had shared together.

"How bout I pick up some Chinese on my way and you can just head over to my place?"

"Sure that sounds great." Grateful that he wanted to her to come over as much as she wanted to. "Don't forget the extra egg rolls." She said happily and she gathered up her stuff.

"Do I ever forget your extra egg rolls?" Mulder asked laughing.

"No I guess you don't." Scully smiled. "Ok well I'm gonna head out and I'll see you in a little bit? She asked.

"Yeah I won't be too much longer. I know I can't leave Dana Scully waiting for food for too long." He said remembering the times he had made her wait and found out Scully gets very hangry.

Mulder watched her walk out the door, happy that they had fallen back into their comfortable relationship. He had been thinking for months now that he wanted to talk to her about their feelings, but he was worried about making things awkward.

_Maybe tonight I'll find the courage._ He thought with a smile and went back to his file.

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Skinner glanced over at the clock on the wall.

5:40pm.

_Great. She should be gone by now._

He grabbed the small envelope he had shoved into his desk when he got in that morning. He wanted to give it to her, more accurately he wanted her to have it, but he didn't want to see her.

He tried to tell himself he didn't care that she could so easily turn away from him and pretend nothing happened between them. He tried not to think about how she felt in his arms and how light his heart felt when he woke up in bed next to her.

Shaking his head he headed to the elevator. He knew the moment they first kissed he was playing with borrowed time and it could, and did, all stop on a dime. That didn't stop him though, from soaking up every ounce of Scully he could.

As the elevator doors opened on the basement floor he thought about going back up. He thought about keeping it, the last piece of her. He knew that was selfish and unfair but he could feel himself torn. Torn between walking out of the elevator and down the hall, and just pushing the button for the first floor. His hand tightened around the small envelope and just as the doors where about the close he stepped out.

No he couldn't keep it. He wouldn't punish her by keeping it, and he would torture himself by holding on to it. It was his last piece of her, and the last evidence of the time they shared and it was time to let it go.

It was time he let go of his hope of being with her again.

He forced himself down the hallway to their office. As he opened the door, intending on leaving the envelope in her desk, he remembered she doesn't have a desk and there was no way he was just going to leave it on the top of the desk for Mulder to find.

Just as he backed out of the office and decided to mail it to her instead, he heard a voice behind him.

"Hey Skinner. You need something?" Mulder asked walking past him into the room.

Skinner mentally kicked himself. Of course Mulder would be working late when he finally decided to give it back to her.

"Ah. No. I just had something to give Agent Scully." He said absence mindly looking down at the envelope he held in front of him.

"Oh she left already I can give it her when I see her." Mulder said taking the envelope before Skinner could react.

"That's ok I can give it to her some other time." Skinner said panicking and trying to take the envelope back.

"No problem Skin-Man. I'm seeing her in a bit." Mulder said grabbing his jacket and heading to the door. "I'll see you tomorrow."

Skinner couldn't move or breathe. In Mulder's hands was pretty damning evidence of his relationship with Scully. He wanted to yank the envelope back, but he knew that would be even more suspicious.

_Maybe Mulder will respect Scully's privacy and not open it._ He thought and hoped as he headed to the elevator. _Maybe this won't all blow up in my face._

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Scully and Mulder sat on his couch with the remaining Chinese food on the coffee table in front of them.

"Scully you still have some egg rolls there." Mulder said smiling at her.

Scully groaned. "No, no more food."

Mulder laughed at her. "Nother beer?" he asked getting up.

"Yeah, thanks."

As Mulder grabbed the beers he saw his discarded jacket and remembered the envelope Skinner had wanted to give Scully. He thought about how awkward Skinner had seemed when he had taken it, and couldn't help but wonder what was in the small envelope.

Walking over he grabbed the envelope and headed back to the living room.

Setting down the beers he started to open the envelope for her. "Hey I forgot, Skin-Man wanted to given this to you but you had already left." He said not looking at her.

Scully could feel her heart drop to her stomach as she watch Mulder open the small envelope. She started to reach for it, but Mulder had already opened it and poured the contents into his palm.

The only sound in the room came from the TV and the sound of their breathing.

Mulder stared at the thin gold chain and small cross that he had seen countless times before. His mind tried to connect the dots and figure out how Skinner had managed to come by Scully's favorite necklace. He kept coming back to one possibility, but he knew that it was rediculous.

Scully stared at the small chain and couldn't move. Maybe she could come up with some explanation of why Skinner could have had it.

_You already told him you lost it. Idiot._

"So. I guess you didn't loose it in your place?" Mulder half said, half asked.

Scully didnt know what to say. She didn't want to out right lie to him, but she didn't want to tell him the truth by any means.

Mulder finally tore his gaze away from the necklace and looked at Scully. Her face was fixed on the necklace. He could see a mixture of emotions on her face. Fear. Guilt. Embarrassment.

"Scully?" He asked

She lifted her head to meet his gaze. She could see the confusion and disbelief in his eyes. _So much for the past staying in the past._

"Scully?"

"I... um...I..." Scully didn't know what to say or even how to start.

Mulder took her hand and laid the necklace in her palm and closed her hand and held it for a moment then let go. Scully looked at her hand and then looked up at him confused. She could see the hurt in his eyes.

"It's late." Was all Mulder said, then he got up and started gathering up the leftover food and taking it to the kitchen.

Scully felt broken. She didn't know how to fix this. She didn't even know if she could. She took a deep breath and stood up and walked to the kitchen when Mulder had yet to return.

She found him rinsing off their silverware.

"Need any help?" She asked, testing the waters.

"No." The short blunt response was all she got.

"Okay." She said softly. She stood watching him for a few moments until it was obvious he didn't want to talk to her.

Scully went back to the living room and slipped on her shoes and pulled on her jacket when she started back to the kitchen to say good bye, Mulder brushed passed her and went to his bedroom.

The only good bye was the slam to his bedroom door. Scully could feel the tears prick the back of her eye lids but she refused to let them fall.

As she locked the door behind her and headed out the of the building to her car she tried to replace her guilt and sadness with anger.

While she was fairly sure Skinner wasn't trying to hurt her on purpose, anger was a much easier emotion to deal with that guilt.

As she started her car she decided if she couldn't talk to Mulder and try and fix this she was going to yell at man that put her in this position. So Scully pulled out onto the road and headed to Skinner's apartment.


	4. Chapter 4

A/N: I'm so sorry this has taken so long for me to upload another chapter!

I hope this lives up to any anticipation you guy's might have had.

As always please comment and review, it lets me know my story is being reviewed well and I'm not going off on an tangent :)

Enjoy!!

-K

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Chapter 4

Scully could feel her anger growing as she made her way across town to Skinner's home. She slammed the car door shut after pulling into a parking spot in front of his place.

As she marched up the sidewalk to his door, she practiced and prepared herself to let him have it for giving her necklace to Mulder. Getting to the door she was about to use the key she had, but decided she wanted to pound on his door instead.

She gave it three good pounds, making her hand sore from the force, then paused for a second or two before pounding again.

She was about to pound for a third time when the door suddenly opened and she had to recoil her hands before punching him in the face.

"What the hell, Dana!?" Skinner asked concerned. "Is something wrong?"

Scully pushed past him and walked into his place. "Yeah, I would say so!" She yelled back. She tossed her purse on the couch as she turned to face him.

For a moment her anger wavered as she liked at him starring at her with some much concern and… something she refused to admit she saw, showing in his eyes.

"Why the hell did you give that to Mulder?" She yelled trying to pull her anger back up. "How could you? Did you do it just to hurt me?" Scully rambled off one accusation after another without so much as a breath in between, and not even letting Skinner answer before throwing another one at him.

Skinner starred at a clearly pissed off Scully standing in his living room yelling and rambling. She spoke so fast he could barely understand what she was saying.

"Dana, calm down-" The moment he said the words he regretted them as her eyes snapped fire at him.

_Never tell a woman 'calm down'. Never tell a woman 'calm down'. Never tell a woman 'calm down'._ He started mentality chanting to himself.

"Calm down? Calm down!?" She yelled as she walked up to him.

Skinner couldn't help but admire that even though with her short stature she barely came up to his chest, she could still hold her own.

"I'm sorry, but what are you talking about?" Skinner asked generally as he reached out to touch her gently. "What's wrong?"

Scully tried to turn and brush him off, in hopes of keeping her anger fired up, but Skinner held her a little tighter not letting her move until she spoke. His genuine concern for her reminded her how she ended up in bed with him in the first place. She started to lower her head feeling her anger falling and leaving her deflated and a little embarrassed for the way she was acting, but Skinner lifted her chin with one finger to make her look at him.

"So are you going to tell me what got you so upset with me?"

Scully took a deep breath as she felt her anger start to rise again.

"My necklace."

Skinner starred at her confused, then took a sharp breath in when he realized what she was talking about, and went out for her so pissed off at him.

"Oh.." He said, starting to take a step back, but this time it was Scully that kept them from moving apart. She looked up at him and Skinner sighed. "I'm sorry. He wasn't supposed to open it." He said trying to explain, "you know, that's kind of rude to open someone else's packages."

Scully laughed a little, "If he knew it was private he wouldn't have."

"Well I could very well have told him it was private or he would have gotten suspicious."

Scully walked over and slumped into his couch. Skinner just walked her for a moment before he went over and joined her.

"I'm really sorry Dana. I didn't plan on him taking it. I just wanted to leave it so you could have it back, but he caught me, and took it saying he was going see you later."

"No, no. I'm sorry." Scully said laying her head back on the back of the couch and closing her eyes. "I shouldn't have come over here all passed off and went off on you. I should have known you would have done that on purpose."

Skinner just watched her for a few moments, soaking up the fact that she was here, with him, so close he could touch her. He had missed her so much the past few months. He tried to get a hold off his feelings but his hand reached out to her before he realized what he was doing. He brushed a stay hair off her face and tucked it behind her ear, and then just let his hand ready on the side of her face.

Scully turned towards him at the touch and let her face rest in the palm of his hand. She gave him a small smile that made Skinner's heart skip a beat.

He knew he should stop whatever was making but he couldn't make himself stop from hoping she might be coming back to him.

Scully could see what Skinner was trying to hide, but it was written all over his face. She hated herself with content she felt with him again.

_Great Dana, have one fight with the man of your dreams and go running back to the sweet, safe guy to feel cared about again!_ She scolded herself.

They say staying at each other for what felt like forever, but what Scully figured was only about five or so minutes.

"I should go." Scully said softly.

Skinner tried to smile at her but it didn't reach his eyes. He stood up with her and walked her to the door.

What they got to the door Scully reached up on her tipy-toes and gave him a quick kiss. It might have been the quickest kiss she ever gave him, but it was enough to break down all the walls and barriers he had been trying to build up. When she turned to walk out the door he finally said what he had been feeling these past few months. Three words that did much more than they literally said.

"I miss you."

Out came out as almost a whisper, with the end barely audible, but she heard. He knew she did by the way she froze with her back to him and her hand on the doorknob, and by the way her head slowly fell down.

Skinner watched her, waiting for a response. For a moment he thought he saw her turn and his heart was jumping for joy.

_She's going to stay! Oh shit what happens now?_ His mind was reaching with all the possibilities, when he finally saw her make up her mind.

She lifted her head, opened the door and walked out.

Out of his life.

Again.


End file.
